Slashdot Mirror
Function of 80% of the Human Genome Charted
ananyo writes "In what is likely to be a historic moment in science, ENCODE, the Encyclopedia of DNA Elements, has published 30 papers in Nature, Genome Research and Genome Biology today, assigning some sort of function to roughly 80% of the genome, including more than 70,000 'promoter' regions — the sites, just upstream of genes, where proteins bind to control gene expression — and nearly 400,000 'enhancer' regions that regulate expression of distant genes. The project was designed to pick up where the Human Genome Project left off. Although that massive effort revealed the blueprint of human biology, it quickly became clear that the instruction manual for reading the blueprint was sketchy at best. Researchers could identify in its 3 billion letters many of the regions that code for proteins, but those make up little more than 1% of the genome, contained in around 20,000 genes. ENCODE, which started in 2003, aims to catalog the 'functional' DNA sequences between genes, learn when and in which cells they are active and trace their effects on how the genome is packaged, regulated and read. Nature has set up an ENCODE site with an explorer, that groups the papers by topic, and collects all the papers, which are available free."
Just happened to hear an NPR interview on the way back to the office. The researcher described most of the 80% as regulating the expression of the protein codes. Brace yourself Slashdot: he called it the 'operating system'.
My God, it's Full of Source!
OUTSIDE_IP=$(dig +short my.ip @outsideip.net)
In three dimensions and with pieces you can't see with your own eyes. Wish em the best of luck.
Wait for the lawsuits when they come across a gene some company holds a patent for. They "invented" it you know.
In what is likely to be a historic moment in science
I'm not knocking the achievement, but wouldn't it be a more truly historic moment when they've nailed down the function of 100% of the genome? Where was the big celebration when they got to 64.576%?
systemd is Roko's Basilisk.
We were told that most of the DNA was junk; you mean the biologists wised up and figured out that nature doesn't deal in junk?
Am I misinterpreting this, or is the usual belief that many genes are obsolete sequences that have no current function being called into question?
Imagine you were given a slightly buggy 3.2Gig piece of software used to run a group of factories and to managing communications between them. You were told to debug this piece of software, but you had no source code, only the machine code only. You could of course observe it's behaviour and set up situations in various factories to see how it behaved. To complicate matters further, you realised that the factories were all performing different functions and making different things but they were all running the same software, but it wasn't immediately obvious why they behaved differently. This is pretty much a huge oversimplification of the challenge that faces modern genetics. We have the assembler language, but we're still not sure entirely what bits are coding sections, which are data sections and which sections are marked up to act as configurations sections. It's a huge task and I love it.
The sky will be the limit.
The understanding of how DNA works, ( and correspondingly, how to hack it ) is the ultimate reverse-engineering accomplishment.
Life is a textbook, full of worked examples. We are at the stage we realize there is an alphabet, the letters mean something, and have the definition of a few words. Kindergarten stuff.
If we play our cards right, and don't spend all our resources fighting amongst ourselves, the future is incredibly bright. We have worked examples of damn near everything we need... photosynthesis ( solar powered CO2 sequestration and energy storage ) for starters. We have bioluminescence, electric eels, and all sorts of sensor examples.
I figure we have been given a huge shipment of arduinos with all sorts of accessories, and we have now figured out how to make the light blink.
We don't know how its wired yet, how the compiler works, and just now figuring out some of what makes the hardware work.
If our society will value knowledge above greed and accounting, if there is anything limiting our potential, I have yet to see it. However if greed and accounting is all we know, we will soon run into all sorts of limits, imposed only by our inability to adapt. First of these will be exhaustion of the earth's fossil fuels, followed by food and water famines. We will be like the chick that hatched, but failed to scratch, find food, and thrive, living off the energy stored in the egg - until it is depleted.
The earth is our egg.
I value highly the knowledge our species acquires. It is our survival.
"Prove all things; hold fast that which is good." [KJV: I Thessalonians 5:21]
See subject.
> It's also got fairly good licensing terms - I mean the OS can be replicated (it is billions of times - once for ever cell), Yeah, right. But use the wrong process for replication, and you'll end up paying for it for almost two decades! How's that for vendor lock-in?
I'll bet that last 20% is where the super powers are.
might be more useful at this point.
They need to figure out how proteins make parts of cells ...
then how parts make cells
then how cells work together to make organs
then how
Seems like understanding something with less layers is required first.
Still, it's amazing how much more they know than a few years ago.
We need to ban patenting of any of this. Our genetic code is our heritage. Companies, and thus people, should not be able to patent genes or their uses. If they want to be rewarded then they need to implement actual therapy and earn their money from that, without any patenting involved.
I'm confused. I thought the non-encoding (junk) DNA was not selected for. That is random mutations were passed on because they evidently did not effect the organism's survival or reproduction. Coding DNA ( genes ) accumulated fewer mutations because mutations adversely effected it or it's offspring's survival.
Now it appears that that non-encoding DNA is important, but seems to be less effected by mutations. Am I missing something?
I think it is made out of much the same stuff up yer 3' end.
Gee after decades of Darwinists proclaiming junk DNA to be key evidence of Darwinian evolution, (before really knowing what those non-coding segments of DNA were for) I wonder what they'll say now. There are more robust theories of evolution than the Darwinian model, but they all suggest design to one extent or another. (In other words, the other theories are honest and don't assert a naturalistic origin for things like DNA)
Glad that someone is doing science!
It will eventually become clear what genes encode the proto-concepts in the brain for mother, father, food, water, etc. Not only that but the concept of the Sun, Moon, and stars will likely have been encoded in there as well. Extrapolate from that notion, you can get Jungian archetypes, a whole catalog of fetishes, and most certainly the predilection towards religiosity.
Bene Gesserit meetup this Sunday.
-- thinkyhead software and media
Four codons map define an ascii char (98 bits). Some stunt earlier this summer had a book encoded into DNA. The storage potential is vast. But the encoding and decoding is as currently rather slow.
It is being selected for to last for some function or another. The truly junk portions probably mutate rapidly within and across species. The so-called "10,000 human genome" database will help elucidate this.
The publication of the ENCODE data is a big deal, make no doubt about it. But it has been overhyped and misreported in the popular press. Interestingly, this is not the fault of science journalists, but rather a consequence of the lead scientists in charge of publicity for this project.
UC Berkeley biologist Michael Eisen has a couple blog posts addressing this issue, as does University of Guelph biologist T. Ryan Gregory. Two of the main criticisms directed at the publicity surrounding ENCODE are:
(1) The fact that noncoding DNA is functional does not count as "news." Far from it. Biologists have known for many, many years that functional elements make up a significant portion of the genome.
(2) The 80% figure, which is being widely reported as the proportion of the genome that is functional, is inaccurate and misleading. A more truthful statement is that 80% of the genome is biochemically active, but this is decidedly not the same thing (a point addressed by Eisen in the second post linked above).
The data produced by ENCODE is extremely important and will lay the groundwork for many future studies. But it should be lauded for that, and not for the hyperbole currently surrounding it.
Whoops... forgot to log in before posting. The publication of the ENCODE data is a big deal, make no doubt about it. But it has been overhyped and misreported in the popular press. Interestingly, this is not the fault of science journalists, but rather a consequence of the lead scientists in charge of publicity for this project. UC Berkeley biologist Michael Eisen has a couple [michaeleisen.org] blog posts [michaeleisen.org] addressing this issue, as does University of Guelph biologist T. Ryan Gregory [evolverzone.com]. Two of the main criticisms directed at the publicity surrounding ENCODE are: (1) The fact that noncoding DNA is functional does not count as "news." Far from it. Biologists have known for many, many years that functional elements make up a significant portion of the genome. (2) The 80% figure, which is being widely reported as the proportion of the genome that is functional, is inaccurate and misleading. A more truthful statement is that 80% of the genome is biochemically active, but this is decidedly not the same thing (a point addressed by Eisen in the second post linked above). The headline on the Slashdot article is completely wrong. The data produced by ENCODE is extremely important and will lay the groundwork for many future studies. But it should be lauded for that, and not for the hyperbole [telegraph.co.uk] currently surrounding it.
Whoops... forgot to log in before posting.
The publication of the ENCODE data is a big deal, make no doubt about it. But it has been overhyped and misreported in the popular press. Interestingly, this is not the fault of science journalists, but rather a consequence of the lead scientists in charge of publicity for this project. UC Berkeley biologist Michael Eisen has a couple blog posts addressing this issue, as does University of Guelph biologist T. Ryan Gregory.
Two of the main criticisms directed at the publicity surrounding ENCODE are:
(1) The fact that noncoding DNA is functional does not count as "news." Far from it. Biologists have known for many, many years that functional elements make up a significant portion of the genome.
(2) The 80% figure, which is being widely reported as the proportion of the genome that is functional, is inaccurate and misleading. A more truthful statement is that 80% of the genome is biochemically active, but this is decidedly not the same thing (a point addressed by Eisen in the second post linked above). The headline on the Slashdot article is completely wrong.
The data produced by ENCODE is extremely important and will lay the groundwork for many future studies. But it should be lauded for that, and not for the hyperbole currently surrounding it.
This definition is broad only if you do not work in any field of biology. For everyone else (the people who actually rely on this research), the definition is absolutely perfect. The author seems to think "functional" means "necessary / beneficial", but for a biochemist knowledge of these "junk compounds" and "junk RNA" is crucial.
tl; dr: this guy is an idiot and seems to think that the ENCODE papers and articles in Nature and the MIT press are aimed at laypeople.