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Function of 80% of the Human Genome Charted

Soulskill posted about 2 years ago | from the scientists-are-busy-busy-people dept.

Biotech 112

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."

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112 comments

But is the first post mapped? (-1)

Anonymous Coward | about 2 years ago | (#41239121)

What is the composition of a first post? If we look into the face of a first post, can we see God?

Re:But is the first post mapped? (0)

Anonymous Coward | about 2 years ago | (#41240905)

I think it is made out of much the same stuff up yer 3' end.

Most of it is control code (4, Interesting)

bill_mcgonigle (4333) | about 2 years ago | (#41239185)

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'.

Re:Most of it is control code (1)

vlm (69642) | about 2 years ago | (#41239311)

I always thought JCL on MVS was more "natural". JCL... its in my genes...

Re:Most of it is control code (4, Insightful)

fm6 (162816) | about 2 years ago | (#41239343)

Yep, and the OS can get reprogrammed by viruses.

Various fields borrow terminology from each other. Not that big a deal. My toaster has a "cancel" button. An old-fashioned "eject" would make more sense to me, but I guess mechanical terminology is less familiar to most people.

Re:Most of it is control code (5, Interesting)

tlhIngan (30335) | about 2 years ago | (#41239581)

Yep, and the OS can get reprogrammed by viruses.

It's also got fairly good licensing terms - I mean the OS can be replicated (it is billions of times - once for ever cell), and the OS can make copies of itself (mitosis), and even end up altering itself through random changes (mutations).

A virus only infects one cell to duplicate itself - all the other uninfected cells have their own copy. The antivirus system basically works by killing infected cells.

So all in all, an interesting OS - security worse than Windows (i.e., none at all - just random strings of genetic code can alter the OS - you don't neve need root! just physical access!), yet it really works by sheer number of copies.

Licensing terms, oh my. (2)

Ihlosi (895663) | about 2 years ago | (#41239771)

> 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?

Re:Licensing terms, oh my. (1)

fm6 (162816) | about 2 years ago | (#41242727)

Bah. You think that's vendor lockin? Consider the same vendor that created this OS also owns the entire universe. Now that is lockin.

Re:Licensing terms, oh my. (1)

mangu (126918) | about 2 years ago | (#41245579)

But use the wrong process for replication, and you'll end up paying for it for almost two decades!

It gets worse. You get liability even if the process is not completed [wikipedia.org]

Re:Most of it is control code (1)

Celarent Darii (1561999) | about 2 years ago | (#41244083)

<blockquote>So all in all, an interesting OS - security worse than Windows (i.e., none at all - just random strings of genetic code can alter the OS - you don't neve need root! just physical access!), yet it really works by sheer number of copies.</blockquote>

Yet just a small mutation can have disastrous consequences for the organism. Just insuring the number of copies is not enough. What is interesting is that the DNA copying process actually prevents 'forking' the source code :

http://www.nature.com/scitable/topicpage/the-dna-replication-checkpoint-and-preserving-genomic-14157692

In fact you need a bit more than 'root' to modify the genetic code. In a certain way DNA has more security than any operating system - imagine that DNA synthesis is going on in your body at several million pairs a sec, and yet you are still the same person. Some operating systems have trouble copying a single file that many times and keeping data integrity.

Re:Most of it is control code (2)

grcumb (781340) | about 2 years ago | (#41240101)

Yep, and the OS can get reprogrammed by viruses.

Various fields borrow terminology from each other. Not that big a deal. My toaster has a "cancel" button. An old-fashioned "eject" would make more sense to me, but I guess mechanical terminology is less familiar to most people.

I'd be a lot more impressed if your toaster had an UNDO button.

Re:Most of it is control code (1)

fm6 (162816) | about 2 years ago | (#41242179)

Jeez, I can't think of any kitchen appliance that wouldn't be improved by such a feature. Alas, entropy is an issue.

Re:Most of it is control code (1)

jedwidz (1399015) | about 2 years ago | (#41242615)

The real innovation wasn't the button label, but figuring out how to turn partly-toasted bread back into fresh.

Re:Most of it is control code (2)

Fallingcow (213461) | about 2 years ago | (#41239443)

So when is the gcc port going to be finished?

Re:Most of it is control code (1)

MrEricSir (398214) | about 2 years ago | (#41239661)

Brace yourself Slashdot: he called it the 'operating system'.

A good start, but wake me up when there's a high-level language that compiles into DNA.

Re:Most of it is control code (1)

Celarent Darii (1561999) | about 2 years ago | (#41244131)

Well, I can do one better - a programming language for DNA computing (so you can not only compile to dna, but even compute with it) :

http://research.microsoft.com/en-us/projects/dna/

a book downloaded into DNA (1)

peter303 (12292) | about 2 years ago | (#41249967)

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.

Re:Most of it is control code (1)

Bob-taro (996889) | about 2 years ago | (#41239885)

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'.

So, can we run Linux?

Re:Most of it is control code (1)

achlorophyl (2205676) | about 2 years ago | (#41241889)

I developed a concept that deals with this.
It's called "genome base one"
it basically means all organisms on Earth, with DNA/RNA, run the same "OS" -- Genome Base One.
We simply have different genomes, and so we are different creatures.
but it's all the same.
I also own the site genomebaseone.com..!

Re:Most of it is control code (1)

Confusador (1783468) | about 2 years ago | (#41244185)

Imagine a beowolf cluster of us! Oh, wait, this is the internet, it's probably been done, with video.

Giant jigsaw puzzle (0)

Anonymous Coward | about 2 years ago | (#41239201)

In three dimensions and with pieces you can't see with your own eyes. Wish em the best of luck.

Wait for the lawsuits (4, Insightful)

viperidaenz (2515578) | about 2 years ago | (#41239221)

Wait for the lawsuits when they come across a gene some company holds a patent for. They "invented" it you know.

Re:Wait for the lawsuits (1)

Anonymous Coward | about 2 years ago | (#41239455)

Mod the parent up -- this is exactly what will happen in the future. If you think the Apple / Samsung battle was bad just wait until major drug companies start battling over which genes their research cores "invented"

We are entering into an interesting century that, according to law, may redefine what it means to be an individual.

Re:Wait for the lawsuits (5, Informative)

whydavid (2593831) | about 2 years ago | (#41239553)

This is probably the single-most important factor in determining whether or not we'll see "personalized medicine" within the next 50 years. The fact that a company owns a patent on the idea of testing the BRCA1 and BRCA2 genes for breast cancer susceptibility is absurd.

Re:Wait for the lawsuits (1)

Cyberax (705495) | about 2 years ago | (#41242393)

The company holds a patent on a specific method of testing for BRCA1/BRCA2 genes. You are free to use any other method, not infringing on their patent. The problem is that the method they've patented is fairly generic, it's possible to work around it, but not cheaply.

Re:Wait for the lawsuits (2)

whydavid (2593831) | about 2 years ago | (#41242681)

My understanding of this is quite different. Look here: http://www.genomicslawreport.com/index.php/2010/10/11/a-do-it-yourself-genomic-challenge-to-myriad-the-fda-and-the-future-of-genetic-tests/ [genomicslawreport.com] If you scroll down to "What This Means, Part I...." there is an explanation of the various patents, including a patent on the nucleotide sequence itself, and the process of comparing the sequence to known mutations. While they speculate that a whole genome sequence would get around the gene nucleotide sequence patents (since you are not sequencing them "in isolation"), you would still need to compare the sequence to known mutations. If that patent is upheld, then it doesn't matter how you go about retrieving the gene. I hope this interpretation is incorrect.

Re:Wait for the lawsuits (2)

Cyberax (705495) | about 2 years ago | (#41242853)

No, situation is more complicated. Myriad has patented the preparation of the affected gene and then detection of mutations. So if you isolate the BRCA1/2 genes and then do testing on them, you'll be likely infringing Myriad's patent.

However, if you sequence/genotype your genome and then check it for BRCA mutations then you're OK and do not infringe on Myriad's patent. That has been affirmed by the court decision (the very same one that upheld the patent claims on BRCA gene isolation process), because the process of aligning and analyzing sequences is not transformative and thus not patent eligible. So yeah, it's a mess, but not as bad as lots of news sources present it.

Historic, or a bit arbitrary? (3)

wonkey_monkey (2592601) | about 2 years ago | (#41239273)

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%?

Re:Historic, or a bit arbitrary? (2)

vlm (69642) | about 2 years ago | (#41239357)

The historic part is its release day. Kind of like that other /. story where gathering 14 million or 13 million or whatever iphone UDIDs into a big pile wasn't the story, the story was releasing them for anyone to look at and download and mess with.

Re:Historic, or a bit arbitrary? (1)

RoknrolZombie (2504888) | about 2 years ago | (#41239395)

You called in sick that day.

Re:Historic, or a bit arbitrary? (1)

thesandtiger (819476) | about 2 years ago | (#41239859)

Maybe not where you work, but at my office we had cake that day.

We have cake pretty much every day, since a bunch of people I work with are insanely avid bakers.

Re:Historic, or a bit arbitrary? (1)

MozeeToby (1163751) | about 2 years ago | (#41239997)

I think it's more along the lines of using everything we know, they mapped everything they could. And now they're done. So current methods can explain some kind of purpose (though I'd be willing to bet some regions have additional uses beyond what was found) for 80% of the human genome. It's possible that the remaining 20% actually does nothing (we know some of it at least is leftover from retro-virus infections for instance) or that it does stuff we don't understand yet or most likely some of each. This is equivalent to the first mapping of the genome in that it's using everything we know to look at the DNA that makes us what we are. They're not done yet, but then, they weren't done after they mapped all the genes either and we still celebrated that.

What about the 'junk' DNA? (1)

fredrated (639554) | about 2 years ago | (#41239297)

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?

Re:What about the 'junk' DNA? (1, Informative)

fuzzyfuzzyfungus (1223518) | about 2 years ago | (#41239361)

If memory serves, 'junk' was some unfortunate-but-persistent description of non-coding regions(which are, indeed, the great majority of the genome); but that work on what exactly the regions that don't code do do has advanced considerably since then...

Re:What about the 'junk' DNA? (0)

Anonymous Coward | about 2 years ago | (#41239373)

Most of it is junk.

-Biologists.

Re:What about the 'junk' DNA? (1)

MightyMartian (840721) | about 2 years ago | (#41239421)

They're called non coding sequences and while many have no perceivable function, some do have regulatory functions. Not to mention that you can get a lot of neutral drift out of those regions.

Re:What about the 'junk' DNA? (3, Informative)

HeckRuler (1369601) | about 2 years ago | (#41239509)

It's time you wised up [wikipedia.org] (it's RIGHT THERE). Junk DNA is non-encoding. Meaning it doesn't get used to make proteins. This was thought to be the entire purpose of DNA, so junk DNA was like commented out code or dead code [wikipedia.org] . But we learned that this genes have other uses. Like some DNA affects the trans-coding of nearby genes. And it appears some non-encoding DNA is still selected for, so it probably has some unknown function.

But nature most certainly deals in junk. And there is DNA in you right now that's non-encoding, non-functional, and not selected for. IE, it's junk. It just happens to be the random uninitialized value or a previous mismatch of old code that was cut long ago. Deal with it.

Re:What about the 'junk' DNA? (0)

Anonymous Coward | about 2 years ago | (#41239985)

But nature most certainly deals in junk. And there is DNA in you right now that's non-encoding, non-functional, and not selected for. IE, it's junk. It just happens to be the random uninitialized value or a previous mismatch of old code that was cut long ago. Deal with it.

Junk like build dependencies or junk like the stuff you get but dont want when you install GNOME?

Re:What about the 'junk' DNA? (1)

anubi (640541) | about 2 years ago | (#41240281)

It looks like some DNA codes for how to make a screw or bolt.

We have a library of what DNA codes for various screws and bolts.

It appears the "junk" DNA codes for where they go.

Re:What about the 'junk' DNA? (1)

Cyberax (705495) | about 2 years ago | (#41242423)

Regulatory regions are small. Together they are probably less than 0.5% of the whole DNA, while _confirmed_ junk is about 66% of the DNA.

Re:What about the 'junk' DNA? (0)

shiftless (410350) | about 2 years ago | (#41242837)

You haven't confirmed shit, other than you're a moron. Looking back in 20 years you'll feel stupid when it turns out that DNA actually does have a use after all.

Humanity and its arrogance. Jesus Fucking Christ.

Re:What about the 'junk' DNA? (2)

Cyberax (705495) | about 2 years ago | (#41242915)

Nope. We HAVE confirmed it. Like, we've analyzed them it turns out that about 33% of the genome consists of simple repeating sequences (SINEs and LINEs). Yep, your genome consists mostly of copy&pasted crap. Oh, then there are about 8% of viral remains and lots of useless LTRs.

They serve no function at all and can be safely deleted without any effect on viability. In fact, pufferfish genome has almost none of them and it has no discernible effect at all. On the converse, plants have in general much more repeated fragments (with great variation between species) and also no discernible effects on their cell viability. But what do I know? After all, my company just produces a novel sequencing method, so it's not like I know what I'm speaking about.

Re:What about the 'junk' DNA? (0)

Celarent Darii (1561999) | about 2 years ago | (#41244187)

"There are more things in heaven and earth, Horatio,
Than are dreamt of in your philosophy. " [Hamlet,1,v]

"No discernible effects on their cell viability" - that is to say, as yet to be discerned. Nature has a way of surprising us, and I dare say that is half the fun. Calling something 'junk' just doesn't do justice to the fact that the organism lives in spite of our lack of understanding it. Calling something 'useless' is really not progressing knowledge in my humble opinion. Better to shelve it off to "don't know yet why it is like this" than to write it off as useless.

In fact in some assembly language programs a NOP is often the most elegant operation, especially if you want self-modifying code.

Re:What about the 'junk' DNA? (1)

HeckRuler (1369601) | about 2 years ago | (#41249465)

This thing with the religious people rallying against the concept of junk DNA seems odd to me. Could someone explain why this is an issue to them?

Re:What about the 'junk' DNA? (1)

Celarent Darii (1561999) | about 2 years ago | (#41250821)

To be honest most of what religious people rally for or against is truly speaking 'junk' in the sense that it is irrational or not understandable. Maybe they think that the world must be perfect in order for their perfect God to exist? Perhaps their notion of God doesn't accept 'felicitous faults'? But really, even the medieval theologians would accept that not everything in the world is ideal. Much of what is called religion today is just emotion, so I do think there is any more of an answer for you than "it insults my dna and or the creator of my dna".

Re:What about the 'junk' DNA? (0)

Anonymous Coward | about 2 years ago | (#41249095)

They serve no function at all and can be safely deleted without any effect on viability. In fact, pufferfish genome has almost none of them and it has no discernible effect at all. On the converse, plants have in general much more repeated fragments (with great variation between species) and also no discernible effects on their cell viability. But what do I know? After all, my company just produces a novel sequencing method, so it's not like I know what I'm speaking about.

YOUR company? No, I guarantee it isn't YOUR company, because if you were smart enough to be the OWNER of such a company, you wouldn't make such idiot statements.

We HAVE confirmed it.

Like I said: you haven't confirmed a fucking thing, other than how stupid and egotistical you are. Now get back to work.

Re:What about the 'junk' DNA? (1)

nashv (1479253) | about 2 years ago | (#41241167)

It's a frozen accident during early attempts to clone genes. When you were cloning genes, you got lots and lots of other non-coding regions into your test-tubes and bacteria that you weren't interested in. Hence , it was called 'junk DNA'. Hence, you know that 'junk DNA' that you get when you try to clone something? Most of the genome is made of that stuff.

It was by no means a statement on the importance of that DNA.

Re:What about the 'junk' DNA? (2)

Cyberax (705495) | about 2 years ago | (#41242443)

Uhm, no. "Junk" DNA is really junk. It consists of repeating regions, transposons, inactive and decaying retroviruses, etc. It has no direct functions, and its indirect usability is questionable. For example, pufferfish has almost no junk DNA while some plants (corn, for example) have lots of it without any visible effects on mutation rates or cell viability.

Re:What about the 'junk' DNA? (1)

nashv (1479253) | about 2 years ago | (#41245779)

That's Francis Crick's interpretation of it. The most popular usage of the term is, however, this : Biémont, Christian; Vieira, C (2006). "Genetics: Junk DNA as an evolutionary force". Nature 443 (7111): 521–4

Re:What about the 'junk' DNA? (1)

bughunter (10093) | about 2 years ago | (#41241437)

Maybe *you* treat *your* DNA like junk, leaving it on the floor or flushing it down the shower drain, and all that.

Biologists treat it like mice and make it run mazes and solve puzzles. They think it's pretty smart.

Junk DNA? (1)

fm6 (162816) | about 2 years ago | (#41239389)

Am I misinterpreting this, or is the usual belief that many genes are obsolete sequences that have no current function being called into question?

Re:Junk DNA? (3, Interesting)

afidel (530433) | about 2 years ago | (#41239549)

Uh, it was called into question over a decade ago. No scientific paper or journal article ever referred to it as "junk" DNA, it was called non-encoding regions and it was understood fairly early on that at least some of the area held a regulatory function. What wasn't realized until the human genome project concluded was just how little of the genome was encoding and how massively important the regulatory regions were (the human body creates a heck of a lot more than 10,000 different proteins so the regulatory regions must be more than simple on/off switches but must also have the ability to affect structural changes in the protein encoding sequence),

Re:Junk DNA? (0)

Anonymous Coward | about 2 years ago | (#41240665)

The thousands of copies of reverse transcriptase were understood to be junk fairly quickly though.

Re:Junk DNA? (0)

Anonymous Coward | about 2 years ago | (#41240939)

It was probably called junk DNA by quite a few papers that tried to show how it had function (or by people who want to get money for funding research on non-coding DNA).

Re:Junk DNA? (0)

Anonymous Coward | about 2 years ago | (#41241039)

It may have been called into question that long ago, but as someone who works in the field, I can tell that from my perspective the "junk DNA" perspective has had a stranglehold in lots of areas.

I can't tell you the number of conversations I've had with colleagues who have dismissed findings--i.e., won't even consider publishing them, or will recommend rejecting papers--because some putative control mechanism is sitting in noncoding DNA.

You're right that this set of papers has been a long time in coming, but it's important not to overtrivialize it either--because much of the scientific community thinks in trivial terms.

Re:Junk DNA? (2)

whydavid (2593831) | about 2 years ago | (#41239635)

Strictly speaking, it is still universally believed that 'many' non-coding genes are historical junk with no current function, and experiments on organisms with much simpler DNA than ours bears this out (in short, they will scramble suspected 'useless' sections of DNA and look for changes in function; impossible to do in humans, but relatively simple for c. elegans). If you are talking about the antiquated view of _all_ non-coding genes as "junk DNA:" This is not the usual belief, at least not in the molecular biology/bioinformatics community. You may just be seeing the release of tons of ENCODE work today, but this research (and a vast amount of related research) has been ongoing for several years. It is well known, and accepted, that many non-coding genes play important regulatory rules in DNA transcription.

Re:Junk DNA? (1)

fm6 (162816) | about 2 years ago | (#41242697)

So, non-coding genes don't create any external proteins, but do help make the genome as a whole work? That still does away with the concept of junk DNA.

Re:Junk DNA? (1)

whydavid (2593831) | about 2 years ago | (#41242791)

If you read what I wrote closely, you would see that what you are suggesting is widely believed to be _not_ true for most non-coding genes. "Junk" DNA is alive and well, though the nice thing about science as opposed to religion is that you won't see a lot of crying if someone conclusively proves that every last nucleotide serves a purpose...but the weight of evidence doesn't support such a conclusion today.

Re:Junk DNA? (1)

tbird81 (946205) | about 2 years ago | (#41245199)

Some DNA codes for proteins.
Some DNA doesn't code for proteins, but regulates expression of other parts of the DNA.
Some DNA has other functions, (e.g to do with mitosis, RNAs etc.)
Some DNA has no function, and is just there because there is no selection pressure to remove it - this can be called junk DNA.

Re:Junk DNA? (4, Insightful)

robotkid (681905) | about 2 years ago | (#41239693)

Am I misinterpreting this, or is the usual belief that many genes are obsolete sequences that have no current function being called into question?

I don't think any serious molecular biologist ever thought the majority of DNA had no function, just as no neuroscientist ever believed that we only use 10% of our brain, but that's precisely the sort of sound bite that, when uttered in a press release somewhere, echos around the public consciousness forever and never dies because it provides a conveniently sciency premise for the next batch of rebooted superhero origin stories. The distinction is that before this study, we knew non-coding DNA was involved in regulation but not to what extent; i.e. there were plenty of specific anecdotal findings but nothing this systematic and large scale.

As for the significance of this sort of work, yes, it exactly like release day for a major software package, it's an anticipatory excitement and not a "we finally found the Higgs Boson after decades of searching" type of achievement. Molecular biologists and geneticists everywhere can now do a simple web search see how this affects the system they are working on without needing to perpetually beg the labs that possess the specialized high-throughput instrumentation to do a one-off experiment just for their favorite gene. . .

Re:Junk DNA? (2)

Cyberax (705495) | about 2 years ago | (#41242511)

Actually, most molecular biologists KNOW that the majority of _eukaryotic_ DNA has no function. It's junk, deal with it. Fairly small parts of non-coding DNA perform useful functions: gene expression regulation (less than 0.1% of total DNA), mechanic 'handles' for cell replication machinery (about 5% of DNA), various RNA enzymes (less than 1%), etc. But most of it is still junk.

Re:Junk DNA? (1)

robotkid (681905) | about 2 years ago | (#41243017)

Actually, most molecular biologists KNOW that the majority of _eukaryotic_ DNA has no function. It's junk, deal with it. Fairly small parts of non-coding DNA perform useful functions: gene expression regulation (less than 0.1% of total DNA), mechanic 'handles' for cell replication machinery (about 5% of DNA), various RNA enzymes (less than 1%), etc. But most of it is still junk.

Sure, it'll never add up to an actual majority of the genome, but do you seriously believe the proportions you quote will still be valid in say, 5, 10 years? Just because something doesn't light up on your nifty hidden markov models doesn't mean there aren't any more epigenetic or non-coding regulatory bits hidden between those mountains of retrotransposon corpses just waiting to be discovered.

Show me a viable cell line with a 90% of the genome removed and then I'll believe you. Until then. . .

Re:Junk DNA? (1)

Cyberax (705495) | about 2 years ago | (#41243101)

Actually, known useless DNA already adds up to the majority (>66%) of the genome. It includes: LTRs (8%), LINEs (17%), SINEs (11%) - that's 45% of known 100% junk. Then we have around 8% of pure viral DNA in our genome (i.e. with remnants of genes encoding viral proteins) - that's already over 50%. And then there are portions of genome with known indirect functions but that don't code anything (padding between proteins, introns, telomeres, etc). In short, over 66% of DNA is known to have no direct functionality.

There was a few surprising discoveries, sure. RNA enzymes were a real shock, for example. All in all, about just about 15-20% of human DNA now has 'putative junk' status that might be changed later with new discoveries.

Re:Junk DNA? (1)

robotkid (681905) | about 2 years ago | (#41243465)

Actually, known useless DNA already adds up to the majority (>66%) of the genome. It includes: LTRs (8%), LINEs (17%), SINEs (11%) - that's 45% of known 100% junk. Then we have around 8% of pure viral DNA in our genome (i.e. with remnants of genes encoding viral proteins) - that's already over 50%. And then there are portions of genome with known indirect functions but that don't code anything (padding between proteins, introns, telomeres, etc). In short, over 66% of DNA is known to have no direct functionality.

There was a few surprising discoveries, sure. RNA enzymes were a real shock, for example. All in all, about just about 15-20% of human DNA now has 'putative junk' status that might be changed later with new discoveries.

You've listed the things we know are useless and pointed out that it adds up to >66%. No argument there. You also hypothesize that there's room for an order-of-magnitude increase in the things that *might* be useful from future, surprising discoveries. That's entirely my point!!

Exactly why are we arguing again?

I can't help but point out, though, that the RNA world folks were all saying "I told you so" when the RNA bits were discovered . . .

Re:Junk DNA? (1)

mc6809e (214243) | about 2 years ago | (#41243599)

Actually, known useless DNA already adds up to the majority (>66%) of the genome. It includes: LTRs (8%), LINEs (17%), SINEs (11%) - that's 45% of known 100% junk. Then we have around 8% of pure viral DNA in our genome (i.e. with remnants of genes encoding viral proteins) - that's already over 50%. And then there are portions of genome with known indirect functions but that don't code anything (padding between proteins, introns, telomeres, etc). In short, over 66% of DNA is known to have no direct functionality.

To suggest that these sequences have no direct functionality is to suggest that somehow they're completely isolated from the chemistry of the cell. That's difficult to prove. And some of what I've read suggests that the physical closeness of some bits of DNA to other bits might be important. Repeats are going to physically shift some parts of DNA relative to others.

How can you be certain these sequences which control the physical relationship of one part of the sequence to another part are completely inconsequential?

Re:Junk DNA? (1)

Cyberax (705495) | about 2 years ago | (#41243737)

Well, we can detect which parts of DNA are transcribed and/or affect transcription. There are multiple ways to do that - we might miss some fine details, but we're pretty sure we're not missing any elephants in the room.

We also know how LINEs and SINEs work on molecular level (i.e. how they propagate within the genome) and we've discovered several mechanisms that inhibit their propagation.

Re:Junk DNA? (1)

fm6 (162816) | about 2 years ago | (#41242675)

That 10% of the brain thing was the usual pop culture nonsense, but I've heard a lot of reputable scientists talk about junk DNA.

Re:Junk DNA? (1)

robotkid (681905) | about 2 years ago | (#41243359)

That 10% of the brain thing was the usual pop culture nonsense, but I've heard a lot of reputable scientists talk about junk DNA.

Yeah the analogy is imperfect but they are both rooted in the common assumption that if we can't assign a function to something then it doesn't do anything at all - which is troubling to me because we don't even know what alot of the "real" genes do yet to do an accurately accounting how much is NOT useful.

So while it'll probably remain true that "junk DNA" will outnumber "useful" DNA in the final accounting (80% is surely a headline-grabbing overreach), there will also continue to be a steady progression of sequences initially tagged as "junk" that turn out to have function. And my initial point was that THAT fact should not come as a surprise to molecular biologists, I can't remember a single year in recent history when there wasn't a discovery of a whole new class of noncoding RNAs, for example.

preserved regions likely not junk (1)

peter303 (12292) | about 2 years ago | (#41250053)

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.

Re:preserved regions likely not junk (1)

fm6 (162816) | about 2 years ago | (#41251437)

You know, I'm grateful to all the people who want to correct my ignorance about "junk" DNA. But I wish the ones who've joined the conversation late would read the previous comments,.

The software analogy (3)

realxmp (518717) | about 2 years ago | (#41239499)

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.

Re:The software analogy (3, Interesting)

HeckRuler (1369601) | about 2 years ago | (#41239721)

Furthermore a long time ago some hackers [wikipedia.org] got in and mucked about committing changes the the trunk. They didn't seem to break anything vital so it was just left alone and we hope it doesn't bite us in the ass before we retire.

Oh yeah, btw, we use a distributed revision control with about 7 Billion [wikipedia.org] branches and no one true trunk (although a lot of people claim otherwise). There's a lot of wanton merging (giggity) and branching, and it seems like every time that happens there's a chance that the revision control just fucks something up [wikipedia.org] and makes a mess of it all.

Re:The software analogy (1)

jedwidz (1399015) | about 2 years ago | (#41242743)

Our backup policy is similarly mind-boggling - we keep this many [answers.com] copies of each branch, but they're all on-site.

Re:The software analogy (0)

Anonymous Coward | about 2 years ago | (#41240137)

Beautiful analogy, realxmp.

Even down to the byte equivalent of the number of base pair our genome is encoded in.

I have over 16 gigabyte of OS in my laptop, and it does only a fraction of what I see living organisms do - and I mean the essences of life itself: reproduction, self awareness, sentience, emotions, greed, love....

The Human Genome Project is the ultimate hack. Our own OS. We are going root now. I feel we are already too close to bricking our civilization as a result of a flaw in our existing OS, which we know as "greed". My prayer is that we find some way of ditching this hindering attribute ( which is to me the incarnation of Satan himself ).

There are those of us who will say without greed, there will be no way of motivating others. I think most of us here on Slashdot know better. We can only be motivated by greed into doing something other than what we were programmed to do in the first place. A musician is going to play, an artist is going to draw, an engineer is going to design. Its our nature. And when those attributes are understood and properly utilized, we will have our utopia.

The cry will come... who will do our dirty work? That's what our engineers are for. We will harness forces in such a manner the desired result is accomplished. Look how many machines already do things no-one takes much pleasure in.

Freedom to be ourselves was the founding notion of America, and I feel the truths still run true, albeit the practice so far has been contaminated greatly by greed and corruption.

When we understand how this works (4, Interesting)

anubi (640541) | about 2 years ago | (#41239571)

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.

Re:When we understand how this works (0)

achlorophyl (2205676) | about 2 years ago | (#41240089)

We fortunately or not will never understand how the human genome works.
Did you know there are about seventy trillion cells in a human body -- and each cell seemingly knows which cell it is? And the body and brain _build_ _themselves_? And when you are wounded, the body _heals itself_?
All this from a data set of only a few billion base pairs? Unlikely. But nature does it.
It is implausible, but apparently not impossible, that DNA/RNA is all there is to ontogeny (growth of the organism).
Each neuron, and there are 100 billion, has on average 1000 interconnections with other neurons -- each one perhaps highly designed, unique and specific.
The idea of no-god is only slightly more absurd than the god-idea.
You have to have faith in something, in this life. May as well be open source software..!

Re:When we understand how this works (1)

benjfowler (239527) | about 2 years ago | (#41240901)

"I don't understand it, therefore God did it"

Derp.

Re:When we understand how this works (1)

achlorophyl (2205676) | about 2 years ago | (#41241239)

More like, "it's not understandable by human limited brains, so to think you can explain it in mortal terms, to mortals, from a mortal, is the ultimate height of human arrogance and false certainty."

Re:When we understand how this works (1)

Rich0 (548339) | about 2 years ago | (#41242331)

Uh, care to prove that it isn't understandable by human limited brains? To suggest that because we don't understand it today we will never know it is a bit arrogant as well.

The genome is finite, as is the complexity of a human. It can be understood.

Re:When we understand how this works (1)

achlorophyl (2205676) | about 2 years ago | (#41243149)

When philosophers of mind say "Nothing worth reading has ever been written on consciousness", they mean it. To say human consciousness is "finite" is simplistic. Really, you don't know how "infinite" it is. After all, we as mathematicians can _conceive _of infinity. Our minds may be the closest things to infinity that anyone ever knows. To pretend to explain them with simplistic strings of DNA is laughable.

Re:When we understand how this works (1)

HeckRuler (1369601) | about 2 years ago | (#41249029)

Well that's adorable but we're not talking about consciousness. I guess it's somewhat nearby the topic at hand, that being understanding how DNA works, because our DNA is pretty important to constructing the brain which is where consciousness resides. But far enough removed that it's still off topic.

But anyway, all sorts of things are "beyond the capabilities of mere mortal minds". Which is why we specialize into narrow fields, approximate, and generally dink around till we get something useful. Even simple things. Yeast for example. All sorts of seriously crazy magical (as in I don't understand it) stuff goes on with yeast. How it's membranes transfer resources in and out of it's cell, and what all it outputs, and how that affects the structure of it's surrounding is all really heady stuff. But even if I'm ignorant of the molecular biology going on, I can still bake bread.

Point is, we do understand how the genome works, enough to be useful, but not completely. We may never fully understand it, but we'll certainly know more than we do now. And it looks like it will happen soon.

Re:When we understand how this works (1)

shiftless (410350) | about 2 years ago | (#41242887)

More like, "it's not understandable by human limited brains

Speak for yourself, peon.

Re:When we understand how this works (0)

Anonymous Coward | about 2 years ago | (#41242279)

"I don't understand it, therefore it doesn't exist"

Re:When we understand how this works (1)

anubi (640541) | about 2 years ago | (#41242543)

You, like I, are in complete awe of the elegance of our design. I like that. I wish more were.

Re:When we understand how this works (1)

HeckRuler (1369601) | about 2 years ago | (#41249331)

Did you know there are about seventy trillion cells in a human body -- and each cell seemingly knows which cell it is?

Yes. Although it's not like they're individually addressable. It's more like every cell knows it's role.

And the body and brain _build_ _themselves_?

Yes.

And when you are wounded, the body _heals itself_?

Yep.

All this from a data set of only a few billion base pairs?

Yes, that's true too. And it's mostly crufty code. (There's also a separate code base for mitochondria)

It is implausible, but apparently not impossible, that DNA/RNA is all there is to ontogeny (growth of the organism).

Oh it's almost certainly true that more than DNA/RNA growing things. That's been known for quite a while. There is genetic information that resides outside of the genetic code [wikipedia.org] . Things like it's structure or those bits that exist in the middle when it's all curled up, those are important even though they're not a base pair.

Each neuron, and there are 100 billion, has on average 1000 interconnections with other neurons -- each one perhaps highly designed, unique and specific.

Neat. (haha, "designed" I see what you did there.) But that's getting off topic, the brain and the structure of how everything is interconnected is developed throughout our lifetime and not entirely dictated by DNA. The DNA describes the system that goes on to build other systems.

The idea of no-god is only slightly more absurd than the god-idea.

Now where the hell did this come from? Are you seriously telling me that because something looks complicated to you that it must mean there's a god?
(hmmm, I guess that explains why the smart cookies are atheists.)

Re:When we understand how this works (1)

rubycodez (864176) | about 2 years ago | (#41243023)

it is more likely that a "defense contractor" with politicians in its pocket will develop awesome bioweapons that will, in a war started for profit or power, extinquish most or all of mankind. Death will be the limit

What about introns? (0)

Anonymous Coward | about 2 years ago | (#41239653)

See subject.

Re:What about introns? (1)

ananyo (2519492) | about 2 years ago | (#41240069)

Introns are parts of genes that are excised before the DNA message gets turned into a protein. So these papers don't have much to do with introns. However, as an aside, it's well known that some introns do have biological functions....
 

Re:What about introns? (0)

Anonymous Coward | about 2 years ago | (#41240157)

Thank you.

The Gaps! (0)

Anonymous Coward | about 2 years ago | (#41240075)

I'll bet that last 20% is where the super powers are.

Understanding 100% of a single cell creature (0)

Anonymous Coward | about 2 years ago | (#41240213)

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.

Ban Genetic Patents (1)

pubwvj (1045960) | about 2 years ago | (#41240293)

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.

Re:Ban Genetic Patents (1)

danhuby (759002) | about 2 years ago | (#41245337)

I would have thought genes have a good deal of 'prior art'.

What about Selection? (1)

InterGuru (50986) | about 2 years ago | (#41240747)

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?

Re:What about Selection? (2)

rnaiguy (1304181) | about 2 years ago | (#41241989)

Just because it doesn't code for protein doesn't mean it isn't turned into RNA, or bound by some protein to regulate some other part of the DNA. Some of it is selected for, we just didn't know where to look to find conservation, or the nature of that conservation. It's easy to pick out regions coding for protein because there are some fairly strict rules for these, so it's easy to find conservation. For some of these non-coding regions, the precise sequence and location is not important, and many similar sequences spread over a wide location range can work just as well. Alternatively, some of these regions are selected to have a certain structure at the RNA stage, which can be satisfied by many different sequences, and undetectable by most methods. Lastly, and most excitingly, these are regions that are evolving quickly. While the function of a protein may remain similar between two species, it may need to be produced in a different time and place in different species. These may be the places in our genetic code where we find out what makes us human. Thus some of these regulatory elements are not conserved between species (though many are!).

Now none of that rules out the existence of regions of DNA that do little or nothing and can be mutated without consequence. There are definitely such regions in the genome.

i hope that cleared something up

Re:What about Selection? (1)

Cyberax (705495) | about 2 years ago | (#41242549)

SOME non-coding DNA has useful functions. Turns out, there's quite a few "RNA enzymes" there and gene expression regulators. They are much more difficult to find then simple genes, because genes generally have predictable "headers". However, most of non-coding is still junk.

Not what Darwinists predicted... (0)

Anonymous Coward | about 2 years ago | (#41241949)

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!

Re:Not what Darwinists predicted... (0)

Anonymous Coward | about 2 years ago | (#41242013)

they all suggest design to one extent or another.

Citation please.

Re:Not what Darwinists predicted... (1)

shiftless (410350) | about 2 years ago | (#41242901)

Not sure if serious

Brace yourselves for the amazingly weird genes... (1)

Slur (61510) | about 2 years ago | (#41244509)

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.

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