ENCODE, hype and junk DNA

Now it's time to take a look at one of the biggest genetic stories this month with science writer, Nell Barrie.  In last month's podcast, I covered a news story about ENCODE, the Encyclopaedia of DNA Elements, which has just been published.  Over the past few weeks, a debate has raged over the findings from the project and perhaps even more so, the way they've been reported.  So Nell, what's going on here?  What is ENCODE?

Nell::  As I understand it, this is a big step on from the human genome project.  That was all about cataloguing all of the DNA code in the human genome and this is about what all of those different bits of DNA actually do.  Are they turning on genes? Are they parts of genes? Are they regulating genes? All of those kinds of questions.  So this is all about finding out what this massive toolkit that we have inside our cells is doing and how it's doing different things inside different types of cells as well.

Kat::  In all the DNA we have in our cells, we have this concept of - I guess it used to be called 'junk DNA' - that there was an awful lot of the genome that wasn't really useful and only a very small percentage is genes.  What do these new studies tell us?

Nell::  Well, the big headline that was coming out over lots of the press reporting was that 80 per cent of the genome is doing something.  And the question became, "Well, what does that actually mean?  What is it actually doing?"  Because it sounded like we were saying, "Most of the genome isn't junk after all" which was exciting in one way, but also, a lot of biologists felt like we already knew that. "Junk DNA" is one of those nice little phrases that doesn't really ring true for a lot of scientists.  It is really interesting because they're trying to find out exactly what all the DNA is doing, but we don't really have enough information yet to know how it all fits together.  So it's almost like, this massive bonanza of information that scientists need to get their hands on and really get to grips with.

Kat::  Because it did seem really exciting.  Well, we've got the genes, but then there's all these bits that switch genes on and switch off, bend around, fold up, do structural things, so that was quite exciting.  It's also really interesting just to see how they've looked into our genomes because I think we think as humans, we must have incredibly special and wonderful genomes.  But just looking at the way they've downgraded how many genes they think we have - do you remember back at the beginning of the human genome project?  Was it 100,000 genes?

Nell:  Yeah, that was they estimated.  They thought that it would turn out humans had about 100,000 genes, and it turned out to be closer to 30,000 which was a bit of a kind of, "Oh, we're not quite as important as we thought we were."  Especially when you compare it to other types of animals which you might think of as simpler, but actually, they have many more genes than we do.  So for example, I was reading today that salamanders have 10 times as much DNA as a human which seems crazy because they're just these cute little amphibians, but that just goes to show how little we know about what are this DNA is actually there for and what it's doing.

Kat::  So, I think they've taken it down to something like 25,000 genes make a human which it doesn't seem like enough when you compare it to how you make other animals or even other kind of plants and other organisms.  But one of the other interesting things about this whole story was the way it was reported because this was a real bonanza for science reporting.  They've published 30 or something papers simultaneously with a website and everything.  Is this a new step forward for publishing science?

Nell::  It certainly seem like that to me and I thought on one level it was great because I looked at this and thought, it's that really exciting, exploratory blue skies type of science where you don't know what you're going to get out of doing this work, but you know it's going to be really interesting and there's probably stuff in there that we don't even realise is going to be important in the future.  So, it's great to show people that side of science and get people excited about it.  But on the other hand, there was this need to come up with these really pithy statements about what ENCODE will do for us, like it will solve all disease, it will tell us exactly what the DNA genome is doing, and obviously, it's not quite there yet.  So I think some of that got a little bit blown out of proportion.

Kat::  Where do you think we go from now with this kind of research and even with this project?

Nell::  Well, I think it's just a case of, all these data is out there now and it's been produced by this consortium which is great because it means that people can have access to it.  Researchers can use the data and they can do whatever they want with.  It's kind of the sky is the limit which just your imagination can determine what you can do with this.  So, it will be really, really exciting to see what comes out of it in the future, but I think that's probably the way we should look at it is it's a tool for future research rather than, this is an amazing research finding right now.

Kat::  And also I think finally, we have to consign the phrase, 'Junk DNA' to the dustbin of linguistics, do you reckon?

Nell::  Yeah, definitely.  There was a lot of commentary on this and I just kind of totally agreed with them and they said, "C'mon, this junk DNA thing really?  We've got rid of our idea already."  It must be there for something or perhaps it was once there for something that it's no longer doing.  But it's just about understanding how everything has evolved over time, how it's still changing.  It's not about saying, "This bit doesn't do anything, we shouldn't be interested."

Kat::  Because it's incredible.  We have over 2 meters of what's basically biological string in every cell of our body, and it's coiled up in such a complicated way.  I mean, I can't believe that much of it would stay in there if it wasn't needed.

Nell::  Yeah, exactly and I think the other thing that I really liked with some of the blog posts I was reading about was this idea that even if you have got DNA that currently isn't doing anything useful, that's almost like the fuel for future mutations.  So, it could mutate and change and suddenly do something quite interesting, and maybe that is the way that's fuelling evolution.  That could be something that's actually quite beneficial in the future.  So, there's a kind of other side to it as well I think.

Kat::  So, thanks very much, Nell.  That's Nell Barrie, Science Writer.