No more "Junk DNA" in Human Genome


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Profile Johnney Guinness
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Message 1280637 - Posted: 6 Sep 2012, 17:02:58 UTC
Last modified: 6 Sep 2012, 17:18:34 UTC

No more "Junk DNA" in Human Genome

Scientists have found 80% of our genome is performing a specific function.

Up to now, most attention has been focused on protein-coding genes, which make up just 2% of the genome.

BBC News; Detailed map of genome function
http://www.bbc.co.uk/news/health-19202141

L.A. Times; ENCODE project sheds light on human DNA and disease
http://www.latimes.com/news/science/la-sci-dna-encode-20120906,0,662375,full.story

Nature journal; ENCODE: The human encyclopedia
http://www.nature.com/news/encode-the-human-encyclopaedia-1.11312

Does anyone here realise the immensity of this announcement? This is one of the greatest scientific announcements in human history!

John.
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Message 1280756 - Posted: 6 Sep 2012, 21:21:45 UTC

Yes :( ish
[rant mode]
No one will be able to afford to give birth.
Before you know it every time a baby is born several corparations will demand large sums of money from the parents for the use of their PATENTED material.
How can it be right for some corp` to patent something that is a naturaly occuring substance in all of us.
[/never ending rant]

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Message 1282633 - Posted: 11 Sep 2012, 14:07:32 UTC

It seems that the author of this article on ArsTechnica seems to think that the claim of "no more junk DNA" is merely marketing due to a change in definitions of what is considered "junk":

The ENCODE project was formed to make sense of that mess. A huge consortium of labs, ENCODE started performing a massive assay of pretty much everything to do with DNA: where proteins stuck to it, how it was packaged, how it was modified, etc. Now, the consortium is out with a massive number of papers—six alone in today's Nature, and dozens to follow in the days to come, scattered through many different journals. The results are staggering: over 1,500 different types of data, assayed across the whole genome, from 147 different cell types. It will feed researchers for years to come.

And it suggests that more of the chaos in the genome may be useful, although that suggestion comes with some big caveats.

First, the data. The researchers used a huge variety of techniques to look at just about anything that can happen to the DNA inside a cell. They took 119 proteins that bind to DNA and found every single site in the genome that they stuck to. They looked for signs of a chemical modification of DNA called methylation that can change the expression of genes nearby. The location of the proteins that structure chromosomes, called histones, were also checked, and areas where the chromosome structure is relatively accessible were pinned down. Regions of the chromosomes that are close to each other inside a cell were mapped. Every single RNA within a cell was sequenced and resequenced.

...

What does it tell us about the genome? Some interesting things, although they're a bit tough to interpret. With data on this scale, we can't actually look at each piece of data on every piece of DNA. So we have to define some generic definitions of things like function: an RNA is made there, a protein binds there, etc. ENCODE chose to go extremely broad: "Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure)." Basically, if anything came out of any of these assays regarding a base, it was considered functional.

And by that definition, most of the genome is doing something. The figure was about 80 percent in these assays, and by adding more cell types, the authors suggest we could get the number even higher.

But there are some problems with that figure. For instance, many of the non-functional viruses and mobile genetic elements will still contain the protein binding sites that used to be critical to their function. So even though these will be traditionally classified as "junk DNA," they'll be considered functional under the ENCODE definition. More generally, proteins that bind DNA are not very picky about their binding sites, so they will create some indication of function by accident; they can also lead to RNA production nearby, looping other bases into an apparent function.


There's another article here on ArsTechnica that discusses the changing in definitions to show that none of this is considered new:

For decades we've known a few things: some pieces of non-coding DNA were critically important, since they controlled when and where the coding pieces were used; but there was a lot of other non-coding DNA and a good hypothesis, junk DNA, to explain why it was there.

Unfortunately, things like well-established facts make for a lousy story. So instead, the press has often turned to myths, aided and abetted by the university press offices and scientists that should have been helping to make sure they produced an accurate story.

Discovery of new regulatory DNA isn't usually surprising, given that we've known it's out there for decades. There has been a steady stream of press releases that act as if finding a function for non-coding DNA is a complete surprise. And many of these are accompanied by quotes from scientists that support this false narrative.

The same thing goes for junk DNA. We've known for decades that some individual pieces of junk DNA do something useful. Introns can regulate gene expression. Bits of former virus or transposon have been found incorporated into genes or used to regulate their expression. So some junk DNA can be useful, in much the same way that a junk yard can be a valuable source of spare parts.

But it's important to keep these in perspective. Even if a function is assigned to a piece of junk that's 1,000 base pairs long, that only accounts for about 1/2,250,000 of the total junk that is estimated to reside in the human genome. Put another way, it's important not to fall into the logical fallacy that finding a use for one piece of junk must mean that all of it is useful.



We haven't suddenly "found" 80% of our genome is performing a specific function; we've known that for decades. This is simply moving the goal posts by changing the definition so that more DNA will be looked at with more scrutiny (from what I can tell).

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Message 1282827 - Posted: 12 Sep 2012, 9:43:48 UTC - in response to Message 1282633.
Last modified: 12 Sep 2012, 9:56:45 UTC

We haven't suddenly "found" 80% of our genome is performing a specific function; we've known that for decades. This is simply moving the goal posts by changing the definition so that more DNA will be looked at with more scrutiny (from what I can tell).

Ozzfan,
I see your point. Some scientists are playing down the announcement, maybe they are a bit jealous of the press publicity the ENCODE project is getting.

But this is big, very big! The term "Junk DNA" came out in the 70's and 80's. And as noted in the ArsTechnica articles, back in the 80's, scientists started finding real function for this so called "Junk DNA". So very slowly over the last 20 years, they started calling it "Non-coding DNA". They found it was preforming "switching" functions. Switching Genes on and off at different times.

But up until the announcement by the ENCODE team the other day, they still had no idea just how much of our DNA had any function. But now they know with great certainty that at least 80.4% of our DNA has some function. And they didn't test all possible cell types. So they know that if they test all possible cell types, they should uncover what the remaining 20% is doing. Of the 3.2 billion base pairs of DNA in our cells, every single bit of it has a function! There is roughly 20,000 protein coding Genes. But there are hundreds of thousands of Genes preforming switching functions.

Its incredible news. I think many scientists will be very jealous of the press coverage the ENCODE team are getting. I think they deserve the good press coverage they are getting. Its the work of over 250 scientists in many countries. Incredible work!

John.
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Message 1282911 - Posted: 12 Sep 2012, 16:40:31 UTC - in response to Message 1282827.

I don't think it's jealousy or a downplaying of the work the geneticists do. It's rightful skepticism toward a media that tends to over-hype all findings that can lead people to believe things that aren't true if they don't have an understanding of science. In this case, people will think, as your title here on SETI@Home suggests, that suddenly there is "No more "junk DNA" in human genome". That's a very sensationalized title that doesn't accurately describe what is going on in the field.

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Message 1282920 - Posted: 12 Sep 2012, 16:58:55 UTC

I agree. Science is not represented faithfully in the mass media. Think of the neutrino affair. Journalists follow the rule "Dog bites man is not newsworthy. Man bites dog is newsworthy".
Tullio
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Message 1282950 - Posted: 12 Sep 2012, 17:30:26 UTC
Last modified: 12 Sep 2012, 17:31:53 UTC

I think the ENCODE team deserve credit, big credit, and big publicity! Its time to reverse the public misconception that some of the code in your DNA is junk. None of your DNA code is junk, none of it!

In one fowl swoop, the ENCODE team have reversed this misconception. From this moment onward, scientists can try to "teach" the public what their DNA is REALLY doing.

Take Introns for example;
http://en.wikipedia.org/wiki/Intron

Introns don't do anything. The don't make anything useful for your human body. But that does not make them "junk". But without the Introns, you would never get any useful proteins. You need the Intron, its critical!

There are hundreds of thousands of Introns in your DNA. Without them, you would never exist!

Its time to teach people about the function of all the stuff that does not directly code for proteins. Everything has a function!

And anyway, the media never explain science properly, thats why they are journalists and not geneticists. The media are trying their best to explain something that is very complex.

John.
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Message 1282954 - Posted: 12 Sep 2012, 17:49:12 UTC - in response to Message 1282950.

No, there's still junk DNA. It's just that some of that junk DNA is still useful in some way. Like the old saying goes, "One man's trash is another man's treasure"; just because it is junk, doesn't mean it is useless.

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Message 1282987 - Posted: 12 Sep 2012, 19:22:15 UTC - in response to Message 1282954.
Last modified: 12 Sep 2012, 19:22:56 UTC

No, there's still junk DNA. It's just that some of that junk DNA is still useful in some way. Like the old saying goes, "One man's trash is another man's treasure"; just because it is junk, doesn't mean it is useless.

Ahhhh comon Ozzfan,
Give them some credit for their hard work. The scientists on the ENCODE team are at the cutting edge of genetic science, over 250 scientists. These guys have worked hard. If they say that 80.4% of the human genome has a function, then it has a function! And they also say that, given time, they will crack the function of the remaining 20%.

This is the cutting edge of science, it always takes many years to get everything perfect. But this is the very best that humanity has at this time.

John.
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Message 1282991 - Posted: 12 Sep 2012, 19:30:30 UTC - in response to Message 1282987.

Johnney, you're taking my comments the wrong way. I'm not trying to take away any credit from the scientists. I'm trying to say that this so-called "news" is sensationalized and somewhat misleading.

The work geneticists do is very important to understanding our very nature. They don't need anyone mis-representing their work through sensationalized headlines, IMHO.

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Message 1283044 - Posted: 12 Sep 2012, 23:35:57 UTC - in response to Message 1282991.

Johnney, you're taking my comments the wrong way. I'm not trying to take away any credit from the scientists. I'm trying to say that this so-called "news" is sensationalized and somewhat misleading.

The work geneticists do is very important to understanding our very nature. They don't need anyone mis-representing their work through sensationalized headlines, IMHO.

I agree with you for a change!

So really its not the scientists that are to blame. Its the journalists fault for blowing things out of proportion.

Fair enough!

John.
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Message 1287575 - Posted: 25 Sep 2012, 3:08:26 UTC - in response to Message 1282950.

I think the ENCODE team deserve credit, big credit, and big publicity! Its time to reverse the public misconception that some of the code in your DNA is junk. None of your DNA code is junk, none of it!

Don't know about yours.
99% of mine is junk.
Want it? LOL?
Actually, do you have any cute single female relatives?

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Message 1287601 - Posted: 25 Sep 2012, 4:44:44 UTC - in response to Message 1287575.

I think the ENCODE team deserve credit, big credit, and big publicity! Its time to reverse the public misconception that some of the code in your DNA is junk. None of your DNA code is junk, none of it!

Don't know about yours.
99% of mine is junk.
Want it? LOL?
Actually, do you have any cute single female relatives?

LOL.....:)

John.

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Message 1291034 - Posted: 4 Oct 2012, 2:58:37 UTC - in response to Message 1287601.

I think the ENCODE team deserve credit, big credit, and big publicity! Its time to reverse the public misconception that some of the code in your DNA is junk. None of your DNA code is junk, none of it!

Don't know about yours.
99% of mine is junk.
Want it? LOL?
Actually, do you have any cute single female relatives?

LOL.....:)

John.


Aged 28 to mid 40s?

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Message 1291053 - Posted: 4 Oct 2012, 4:46:18 UTC

Thanks for the link to this thread from another one Johnney. I'd heard about this research on a recent broadcast of Radio 4's In Our Time. While some might take issue with equating ENCODE's "some function" with "genes", I'm more interested about why you believe the discovery to be particularly significant.
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Message 1291163 - Posted: 4 Oct 2012, 13:11:41 UTC - in response to Message 1291053.
Last modified: 4 Oct 2012, 13:16:14 UTC

Thanks for the link to this thread from another one Johnney. I'd heard about this research on a recent broadcast of Radio 4's In Our Time. While some might take issue with equating ENCODE's "some function" with "genes", I'm more interested about why you believe the discovery to be particularly significant.

Hi Bobby,
I'm glad to "discuss" genetics with you any time. But i won't get into a "debate" with you that just goes around in circles.

The term "Junk DNA" has been bandied about for the last 30 years as a "tool" evolutionists and Darwinists use to "prove" the case for evolution being true. This "tool" is now gone!! No evolutionist or Darwinist can ever again use the term "Junk DNA" as a proof that humans evolved. But there is also a flip side to this!

Bobby if you really did understand genetics, which i know you don't, then you would understand that this announcement by the ENCODE team is proof that human beings were created by an intelligent designer, or scientist, or God as he is better known in the western world.

Bobby i know by peoples reaction to this thread that the people who hang out on this forum don't understand the implications of the announcement by the ENCODE team. If people understood the announcement, if the general public understood the announcement, then they would know that they had found proof of God. The proof is written in our genes. But because genetics is so complex, 99.99999% of people just don't understand it. In fact many of the geneticists who work on the ENCODE project don't understand the implications themselves. Some of them do understand, but they are staying quiet!

Bobby, to help you understand this better. If we "slowly evolved from monkeys" over a long period of time, this would have altered tens of thousands of "base pairs" on the human genome. It would also have given us tonnes of "Junk DNA", maybe hundreds of thousands of base pairs of Junk. But that is not what the ENCODE team found. The have plotted "function" for over 80% of the human genome, and they also report that, within a few years, they will have found the function of the other 20%. As a result of this, slow evolution over thousands of years is absolutely 100% impossible. And Bobby the only way you could argue with this finding is if you don't understand genetics.

Bobby, even if you hate the thought of it, even if you revile religion, even if are horrified by the thought of a God, the scientific fact is that you Bobby, and Me, were both created by a creator. This creator would have to be a scientist. And he "created" the genes that make up your's and my ancestors. It happened exactly like it says in the Christian Bible. Its is scientific fact, its not speculation. Bobby i know this because i study genetics full time. This is what i do with my time. I study human genetics, and i'm becoming very good at it. I'm not an expert in genetics, but i have an above average understanding of genetics.

Bobby, i'm like a teacher. I will help you to learn if you choose to learn. But you have to "choose" to want to learn why this announcement proves we were created and we didn't evolve. I won't argue it with you. If you want to argue, go somewhere else or start a different thread.

John.
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Message 1291199 - Posted: 4 Oct 2012, 15:03:13 UTC - in response to Message 1291163.

Thanks for the link to this thread from another one Johnney. I'd heard about this research on a recent broadcast of Radio 4's In Our Time. While some might take issue with equating ENCODE's "some function" with "genes", I'm more interested about why you believe the discovery to be particularly significant.

Hi Bobby,
I'm glad to "discuss" genetics with you any time. But i won't get into a "debate" with you that just goes around in circles.

The term "Junk DNA" has been bandied about for the last 30 years as a "tool" evolutionists and Darwinists use to "prove" the case for evolution being true. This "tool" is now gone!! No evolutionist or Darwinist can ever again use the term "Junk DNA" as a proof that humans evolved. But there is also a flip side to this!

Bobby if you really did understand genetics, which i know you don't, then you would understand that this announcement by the ENCODE team is proof that human beings were created by an intelligent designer, or scientist, or God as he is better known in the western world.

Bobby i know by peoples reaction to this thread that the people who hang out on this forum don't understand the implications of the announcement by the ENCODE team. If people understood the announcement, if the general public understood the announcement, then they would know that they had found proof of God. The proof is written in our genes. But because genetics is so complex, 99.99999% of people just don't understand it. In fact many of the geneticists who work on the ENCODE project don't understand the implications themselves. Some of them do understand, but they are staying quiet!

Bobby, to help you understand this better. If we "slowly evolved from monkeys" over a long period of time, this would have altered tens of thousands of "base pairs" on the human genome. It would also have given us tonnes of "Junk DNA", maybe hundreds of thousands of base pairs of Junk. But that is not what the ENCODE team found. The have plotted "function" for over 80% of the human genome, and they also report that, within a few years, they will have found the function of the other 20%. As a result of this, slow evolution over thousands of years is absolutely 100% impossible. And Bobby the only way you could argue with this finding is if you don't understand genetics.

Bobby, even if you hate the thought of it, even if you revile religion, even if are horrified by the thought of a God, the scientific fact is that you Bobby, and Me, were both created by a creator. This creator would have to be a scientist. And he "created" the genes that make up your's and my ancestors. It happened exactly like it says in the Christian Bible. Its is scientific fact, its not speculation. Bobby i know this because i study genetics full time. This is what i do with my time. I study human genetics, and i'm becoming very good at it. I'm not an expert in genetics, but i have an above average understanding of genetics.

Bobby, i'm like a teacher. I will help you to learn if you choose to learn. But you have to "choose" to want to learn why this announcement proves we were created and we didn't evolve. I won't argue it with you. If you want to argue, go somewhere else or start a different thread.

John.


We didn't "slowly evolve from monkeys", at least that's not the currently held scientific view (aka the best current approximation). The best current approximation of science is that we share a common ancestor with the great apes, and the most recent divergence leading to extant species was with chimpanzees. The great apes certainly do have a common ancestor with monkeys, all mammals have a common ancestor according to the best current approximation.

The term "Junk DNA" is not part of the vernacular of the best current approximation, the term used there is "noncoding DNA", and the ENCODE discovery does not change the label. Noncoding DNA is not unique to homo sapiens sapiens, it's found in all extant species. It's called noncoding because it does not contain a "blueprint" for protein fabrication.

Noncoding DNA has been found to be subject to evolutionary pressure, so it's been clear that it was more than just "junk" for many years, the ENCODE discovery appears to provide a better understanding of its role, though it's not the fundamental shift in the understanding of genetics that you appear to believe it is.

Thanks for describing why you believe the discovery is important. As you may be able to gather, I don't share your belief, and, given your reasons, see no reason why I should. It seems to me that many of the popular press articles on the ENCODE discovery share common traits with much of the popular press's portrayal of scientific discoveries, they are over simplified and over hyped. Both traits appear to hinder rather than help an understanding of science.

Johnney, if you really did understand genetics, then you would understand that this announcement by the ENCODE team is not proof that human beings were created by an intelligent designer, or scientist, or God as he is better known in the western world. Though you would understand that the discovery is the latest of many that help us understand how natural processes have resulted in the biodiversity we see about us today.
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Message 1291205 - Posted: 4 Oct 2012, 15:16:56 UTC

Bobby, i'm like a teacher. I will help you to learn if you choose to learn. But you have to "choose" to want to learn why this announcement proves we were created and we didn't evolve. I won't argue it with you. If you want to argue, go somewhere else or start a different thread.

Reading between the lines here that seems to me to indicate that, if you don't want to believe what I believe then I'm not interested in talking to you. I hope you didn't mean that.

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Message 1291206 - Posted: 4 Oct 2012, 15:19:07 UTC

Then i guess we disagree Bobby. Best leave it at that so.

Thanks,
John.

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Message 1291209 - Posted: 4 Oct 2012, 15:27:13 UTC - in response to Message 1291205.
Last modified: 4 Oct 2012, 15:31:26 UTC

Bobby, i'm like a teacher. I will help you to learn if you choose to learn. But you have to "choose" to want to learn why this announcement proves we were created and we didn't evolve. I won't argue it with you. If you want to argue, go somewhere else or start a different thread.

Reading between the lines here that seems to me to indicate that, if you don't want to believe what I believe then I'm not interested in talking to you. I hope you didn't mean that.


Chris,
No, it means that i don't want to "debate" the issue. But i am willing to "discuss" the issue, and teach. I'm tired Chris, i'm very tired from the work-load i have taken on.

If a 5 year old child goes to school, the teacher will try to teach the child the A B C's. What would happen if the child rejects learning English, debates the validity of the English language and demands that he be taught Egyptian hieroglyphics instead? --- If i was this child's teacher, i would not get involved in this child's "debate". Instead i would throw the child out of the class and i would teach English to the children who choose to cooperate and learn what is being taught. Bobby wants to "debate", i don't. I want to either learn new things, or teach what i already know.

John.
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