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Confusion and Criticism Over ENCODE's Claims

Unknown Lamer posted about 2 years ago | from the everyone-had-too-many-cheetos dept.

Science 34

As_I_Please writes "In response to the previous report of the ENCODE project discovering 'biochemical functions for 80 percent of the genome,' many scientists have questioned what was meant by 'function.' Ars Technica Science Editor John Timmer wrote an article calling ENCODE's definition of functionality 'broad to the point of being meaningless. At worst, it was actively misleading.' Nature magazine also has a followup discussing the ambiguity surrounding the 80% figure and claims about junk DNA."

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no confusion about who got that frost (-1)

Anonymous Coward | about 2 years ago | (#41313673)

wat wat

frosty piss (1)

hoboroadie (1726896) | about 2 years ago | (#41313729)

Patent Trolls seem analogous to /.

I used to care about science journalism (4, Insightful)

BMOC (2478408) | about 2 years ago | (#41313773)

...and then climate change happened.

Since then I just started reading abstracts/papers rather than the journalism. It takes a little longer, but at least I'm not being misled by some self-aggrandizing social-science major who chose his degree poorly and is now trying to just pump out stories in time for the weekend.

/yes, I'm bitter. But seriously, screw science reporters.

Re:I used to care about science journalism (0)

Anonymous Coward | about 2 years ago | (#41314623)

What confusion? First lines in Nature http://www.nature.com/nature/journal/v489/n7414/pdf/nature11247.pdf are as clear as the collapse of Twin Towers; both JunkDNA and Central Dogma are history. True, incredible dust followed. Also there were plenty of warnings; read 310 on Slashdot a Decade ago: http://thinkgeek.shill.slashdot.org/index2.pl?fhfilter=pellionisz

Re:I used to care about science journalism (4, Interesting)

Anonymous Coward | about 2 years ago | (#41315149)

No, neither junk DNA nor the Central Dogma are history. People misquote the Central Dogma all the time as something dubious like "DNA -> RNA -> proteins," but that is not what the Central Dogma says. This is the central dogma as stated by Francis Crick in 1958:
once (sequential) information has passed into protein it cannot get out again.
IOW, information can flow back and forth between DNA and RNA, but once it gets into protein, it can't go back. This was stated in 1958, and it's STILL TRUE today. But there are science history revisionists and mediocre science journalists that keep pretending that the Central Dogma states "DNA -> RNA -> proteins," and then when some scientists discovers RNA information going to DNA, they declare the Central Dogma "dead" like you have here.

Junk DNA is NOT dead either. We KNOW for a fact that there are pseudogenes and transposons that do nothing, It's debatable how much of our genome is made up of this, but there's no denying that junk DNA exists. It's not simply an argument from ignorance ("we don't know what it does, so we conclude it does nothing"). There are a number of positive arguments that can be made for junk DNA, including looking at conserved v. non conserved sequences, comparing the proportion of alleged junk DNA regions in the genomes of different organisms like pufferfish (who have very little of it) and onions (which have a lot). It's also been noted that synthesizing a completely fake and artificial strand of DNA and subjecting it to ENCODE style tests would yield false positives, so the ENCODE study does very little to refute junk DNA.

Re:I used to care about science journalism (2)

oldhack (1037484) | about 2 years ago | (#41315641)

Don't leave out the researchers. They seem intent to "play the game" right along with the reporters and PR flunkies.

Re:I used to care about science journalism (1)

BMOC (2478408) | about 2 years ago | (#41315769)

Yes... but please stop ruining my day further...

*cries*

The selfish gene. (2)

Hatta (162192) | about 2 years ago | (#41313787)

The idea that junk DNA accumulates on its own, only because of it's propensity to replicate is expected from evolution. If it replicates, and it's not selected against, it will accumulate. Some of it may have a function, and that which does have a function will be preserved, but that doesn't mean it all has a function.

If it were discovered that every single base pair in our DNA had a function, that would be very strong evidence against evolution by natural selection.

Sounds more like fighting over sacred cows (1)

medv4380 (1604309) | about 2 years ago | (#41313805)

I'll agree that the 80% figure is probably just PR hype, but part of the argument seems to be the notion that only 1% of our DNA codes for Proteins and that's the only important part. I believe that notion has already been discredited with epigenetics, and unless I'm mistaken that is the reason for the ENCODE Project in the first place.

Re:Sounds more like fighting over sacred cows (1)

MozeeToby (1163751) | about 2 years ago | (#41313947)

No, we've known for a long time that some of the 'junk' DNA has instructions for gene activation and deactivation, pretty much since the discovery of 'junk' DNA in the first place. The problem is that ENCODE's 80% figure assumes that any piece of DNA that produces RNA performs a biological function which is extremely misleading. A lot of that RNA will never be used for anything. A lot of it will be immediately destroyed after it's created.

Re:Sounds more like fighting over sacred cows (5, Informative)

tehdaemon (753808) | about 2 years ago | (#41313955)

No - it is not hype - it is a misunderstanding of the definition of 'functional'

I buy a box of bolts at the hardware store. They have no manufacturing defects, and no damage. They are still in the box. Are they functional?

Yes - If I take a nut and try to thread it on the bolt, it works, if I try to screw it into a hole, it works.

No - They are not currently holding any parts of any kind together, they don't form any part of any useful machine - they are not functional.

The ENCODE project is using the first definition. 80% of the DNA produces RNA, or has binding sites that bind to regulatory proteins, or some other function that can have a real impact on the cell. Whether or not the RNA is actually used, or if the regulatory sites actually regulate something, or if it actually has an effect on the cell was not considered - and is probably not known yet for most of that 80%.

Most people when they hear 'functional DNA' assume that it has an impact on the organism. The ENCODE project is working on a lower level, asking, 'Does this DNA do something on a molecular level?' not 'Does this DNA make a difference to the cell?'. That is of course the next question, but they are not there yet.

T

Re:Sounds more like fighting over sacred cows (1)

cfulton (543949) | about 2 years ago | (#41314137)

This is the best explanation for the 80% figure that I have seen. I've been reading a bunch of the articles out there about this and none of them made such a clear and useful analogy. Please Mod Parent Up.

Re:Sounds more like fighting over sacred cows (0)

Anonymous Coward | about 2 years ago | (#41314975)

"part of the argument seems to be the notion that only 1% of our DNA codes for Proteins and that's the only important part. I believe that notion has already been discredited with epigenetics"

It's been known for decades by molecular biologists and biochemists that non-coding DNA can have a function, so this isn't something that was recently "discredited." The proponents of junk DNA have NEVER claimed that only protein coding DNA is functional.

Isn't it obvious? (2)

crow (16139) | about 2 years ago | (#41313815)

So we understand how somewhere on the order of 20% of the DNA works. It encodes proteins. What we don't understand is how things like body structure and aging work. Clearly those are part of the DNA, so it seems obvious that there's some sort of switching process going on using at least some of that other 80%.

Once we figure out how the chemistry of that programming works, we can start to decode the fractal patterns that define body structure.

Of course, we will find that there is true junk DNA--think of code blocks that can't be reached. How much evolutionary dead code is left in there may be an interesting academic question.

Re:Isn't it obvious? (0)

cfulton (543949) | about 2 years ago | (#41314347)

We know and have known for a long time about some if not all of the regulatory function in DNA. The first description of non-coding DNA playing key regulatory roles in activation was in 1959 when the Lac operon was discovered by François Jacob and Jacques Monod for which they won the Nobel Prize. Many other regulatory sequences have been discovered since then. Other types of genetic operators such as transposons which are able to transport and duplicate blocks of DNA are known. This is the problem, we know a lot about the complexity and function of DNA. We understand that it does much more than simply code proteins. But, the popular press continues to act as if it is a giant surprise whenever any other function is discussed.

No. Just no. (2)

shiftless (410350) | about 2 years ago | (#41317493)

This is the problem, we know a lot about the complexity and function of DNA.

No, the problem is, you think you do when in reality you don't know shit. Future generations will look back on your pronouncements of "knowing so much" about DNA to be as laughable as us hearing stories of professors back in the 1930s who claimed all the important stuff had been discovered, and that there is nothing useful left to research into. In other words, dead wrong, ignorant, and stupid.

Re:No. Just no. (0)

Anonymous Coward | about 2 years ago | (#41318989)

Knowing a lot is quite different than claiming to know everything... cfulton had a good point that journalism frequently acts like any research in that field is a major discovery due to assuming such DNA had zero function beforehand. It obscures whether such research is actually a big discovery or not. This isn't saying the field has been finished and research stopped, as there is still a long ways to go.

Re:No. Just no. (0)

Anonymous Coward | about 2 years ago | (#41320643)

No, the problem is, you think you do when in reality you don't know shit. Future generations will look back on your pronouncements of "knowing so much" about DNA to be as laughable as us hearing stories of professors back in the 1930s who claimed all the important stuff had been discovered, and that there is nothing useful left to research into. In other words, dead wrong, ignorant, and stupid.

Your comment is utterly absurd hyperbole, and it is also bside the point. Taking it to its logical conclusion, we should disregard everything we know about anything because there's so much more out there we don't know. Let's call quits on the whole scientific enterprise instead of kindling a small light in the vastness of our ignorance.

The reality is cfulton is correct. We have known for quite some time that some non-coding DNA has a function. This 1) does not imply that ALL of it has a function, and 2) for the ENCODE scientists and other anti-junk DNA proponents to claim that we didn't know this so they can pretend they've made a monumental discovery is absurd and worthy of criticism.

Of course the fact that we know something about DNA doesn't mean we claim to know everything about it. There's still a lot to discover, but the evidence for things like the lac operon and other regulatory sequences is well entrenched in the literature (not to mention duplicated in undergraduate labs in a standard molecular biology class), so it is absurd to deride it as unknown and for you to ignore it while waxing general about the nature of absolute knowledge, which is a discussion of epistemology that is utterly beside the point.

Re:No. Just no. (1)

shiftless (410350) | about 2 years ago | (#41331651)

Your comment is utterly absurd hyperbole, and it is also bside the point. Taking it to its logical conclusion, we should disregard everything we know about anything because there's so much more out there we don't know. Let's call quits on the whole scientific enterprise instead of kindling a small light in the vastness of our ignorance.

No, dummy, you expertly missed the point. Hyperbole? I'm comparing what you're doing now to things which actually happened! You cannot engage or refute my analogy because it is factually correct. Then after accusing me of hyperbole you then of course laugh directly into it yourself, speaking to absurdity. Of course we should learn all we can. But when we arrogantly start assuming we know everything, that's always when Nature will decide to bitch slap us. Haven't you ever seen Titanic?

Re:Isn't it obvious? (1)

Anonymous Coward | about 2 years ago | (#41315409)

So do we really know that it's DNA that does aging?

Re:Isn't it obvious? (0)

Anonymous Coward | about 2 years ago | (#41318003)

Something about telomeres?

Re:Isn't it obvious? (1)

Anonymous Coward | about 2 years ago | (#41318725)

Decrease in telomere length, (amongst other things...etc. :D) is currently big in ageing research, etc.
http://en.wikipedia.org/wiki/Telomere#Telomere_shortening [wikipedia.org]

And I would agree with the poster who rather vulgarly stated that 'we don't know sh.t' We are in the stone age of genetics, etc. We know next to nothing, and a pretension to 'knowledge' is indeed an age old problem...lol...:D

Unfortunately, I don't have much time to brutally interrogate those who think 'we know a lot' to demonstrate how little they know...about anything...
LOL! :D (ah, Socrates, where are you when we need you? LOL! 'All I know is that I know nothing')

To understand how DNA works over time, we are just beginning to use techniques such as microarrays to study when/where/how genes are activated/deactivated, etc. over time, etc.

http://en.wikipedia.org/wiki/DNA_microarray [wikipedia.org]

It will be centuries before anyone can remotely say we 'know alot' about DNA, etc. LOL! :D

in other news (1)

zlives (2009072) | about 2 years ago | (#41313839)

an article calling ENCODE's definition of functionality 'broad to the point of being fully patentable'
let the human gnome patent trolling begin.

Apple Rules The World! (-1)

Anonymous Coward | about 2 years ago | (#41313887)

And to think you don't have an Apple? You are by definition: A looser.

A looser definition (0)

Anonymous Coward | about 2 years ago | (#41314543)

We get the full range on /.
Troglodytes, morons, imbeciles, idiots, trolls, et cetera.

Science by press release (0)

Anonymous Coward | about 2 years ago | (#41314833)

It's really sad that much of the public get their scientific beliefs from misleading press releases that lead to utterly incorrect headlines and stories in the popular media, and the ENCODE consortium should be ashamed of themselves. They've done lots of damage that many other scientists will have to spend time and effort to correct.

Bravo to Ars for publishing this valuable corrective, but I'm afraid that the damage has already been done. ENCODE was last week's news. People have assimilated the soundbite about 80% of the genome being functional (which probably merely seems like common sense to those with little or no knowledge of our genetic history and the processes that are known to shape the genome), and have now moved on.

The fact that their definition of 'functional' was utterly preposterous is a detail that will be overlooked, along with the rest of the work the consortium carried out.

The best suggestion I've heard is for the ENCODE scientists to produce a few hundred megabases of random DNA, then test this to see how much would be 'functional' by their definition (my prediction - lots of it). Then we'd have a useful negative control and baseline.

There are also other nice rebuttals out there if people care to google for them.

Favorite quote from the article (1)

gameboyhippo (827141) | about 2 years ago | (#41315059)

"Several researchers took issue with ENCODE’s suggestion that its wobbly 80% number in any way disproves that some DNA is junk. Larry Moran, a biochemist at the University of Toronto in Ontario argued on his blog that claims about disproving the existence of junk gives ammunition to creationists who like a tidy view of every letter in the genome having some sort of divine purpose."

Translation: I don't believe it because it conflicts with my beliefs. Where have I heard that before?

Re:Favorite quote from the article (0)

Anonymous Coward | about 2 years ago | (#41315559)

Actually, Larry Moran provides ample reasons and evidence why ENCODE's claims are problematic, not the least of which is their incredibly dubious definition of function as anything that's active at the molecular level. Under that very trivial definition, all of DNA is functional, since all of it interacts with replicase during replication. Oh, and all of it bumps into water molecules at some point, so hey, that's a function too. Oh, don't forget that DNA adds mass to the cell. There's a "function." Of course, if you could be bothered to read what the scientists who have objected to ENCODE's conclusions have to say, you'd find that they don't simply say "it conflicts with my beliefs so I refuse to believe it." Nice strawman though.

Re:Favorite quote from the article (1)

HeckRuler (1369601) | about 2 years ago | (#41316667)

uh, maybe, but when they say function I think they mean something with a little more impact [wikipedia.org] . Things that are actually selected for. You know, natural selection. This functional non-encoding DNA was known about before they came out with these papers.

Not that I'm a pro or anything, but junk DNA was anything that didn't encode proteins, right? And previously it was thought that encoding proteins was the entire purpose of DNA. Well now they found additional function of the non-encoding DNA. And these ENCODE papers hammer it home I guess?

Not that there isn't still junk DNA that isn't doing anything. All that virus code muddled about in there probably isn't helping us out any.

Re:Favorite quote from the article (0)

Anonymous Coward | about 2 years ago | (#41320711)

Not that I'm a pro or anything, but junk DNA was anything that didn't encode proteins, right? And previously it was thought that encoding proteins was the entire purpose of DNA. Well now they found additional function of the non-encoding DNA. And these ENCODE papers hammer it home I guess?

Nah, "junk DNA" was not coined to refer to DNA that didn't encode proteins. The phrase "junk DNA" was coined by Susumu Ohno in 1972, a time when scientists already knew and were fully aware that some non-coding DNA had function. At the time, Ohno offered an argument for the existence of junk DNA (that is DNA with a sequence that isn't vital to the operation of the organism) based on mutational load, an argument which is still valid and unrefuted to this day, so be wary of any crackpots that tell you junk DNA has been refuted, and be wary of ENCODE scientists hyping their findings for media attention.

Re:Favorite quote from the article (1)

CTachyon (412849) | about 2 years ago | (#41320947)

Not that I'm a pro or anything, but junk DNA was anything that didn't encode proteins, right?

No, that's "non-coding DNA". The Ars Technica article has a very nice Venn diagram. In short, we infer that most non-coding DNA is junk DNA because it shows signs of neutral drift (i.e. it doesn't matter to reproductive fitness), but non-coding DNA is different from junk DNA, and regulatory DNA is always non-coding but can be either junk or non-junk.

Some concrete examples (with Venn diagram colors in parens):

  • Coding DNA that isn't junk (white): a gene.
  • Coding DNA that is junk (blue): an endogenous retrovirus.
  • Regulatory non-coding DNA that isn't junk (orange/yellow): a promoter for a gene.
  • Regulatory non-coding DNA that is junk (orange/yellow/blue): a promoter for a pseudogene.
  • Non-regulatory non-coding DNA that isn't junk (yellow): hmm... an intron, I guess.
  • Non-regulatory non-coding DNA that is junk (yellow/blue): the letters "CGG" 30 times in a row on the X chromosome. (See aside below for more info.)

(Terminology: a "pseudogene" is a gene damaged so badly by frame shifts or early stop codons that it can't code for protein anymore. Before they break and become pseudogenes, they're often duplicates of some existing gene, which is why breaking them can be fitness-neutral. DNA transposons and sloppy cross-overs in meiosis make gene duplication reasonably common. Gene duplication is important for evolution as well: duplicated genes are free to mutate in random directions until they stumble on a new useful function, with the original free to keep the old one. For instance, the vertebrate blood clotting cascade was clearly formed from several rounds of dupe-then-mutate, and similarly with the huge family of myosin muscle proteins.)

(Terminology: an "intron" is a stretch of DNA that gets snipped out of the resulting RNA before the RNA can code for protein. It's not quite junk: an intron has recognition signals that say "please cut RNA here", and IIRC the intron needs to have roughly the correct length, but most of the intron is arbitrary nonsense. Some genes have alternative splices, where the same gene can code for different proteins by swapping in different coding regions -- "exons" -- like lego bricks. Alternative splices are important in the immune system, for instance: they're how antibodies work. And the alternative splicing stuff wouldn't be possible without introns, including the nonsense filler that helpfully spaces out the exons so the splice enzymes can operate correctly.)

(Aside: long sequences of repetitive DNA can trip up the DNA polymerase enzyme that copies DNA, causing the stretch of DNA to lengthen itself in the next generation... and the longer it gets, the better the chance is that DNA polymerase will screw up and make it longer still. The ...CGG-CGG-CGG... sequence I mentioned has about 30 repeats in healthy individuals; but if the number of repeats climbs high enough, it causes Fragile X syndrome [wikipedia.org] . Apparently the nucleus tries to silence the repeat by attaching methyl groups (CH3), which is standard procedure in the nucleus for turning off misbehaving DNA, but methylation isn't terribly precise and a nearby promoter happens to live nearby. This promoter is responsible for a nearby gene that's important in brain development; if the promoter is silenced by methylation, the reduced gene expression causes a form of severe autism.)

Re:Favorite quote from the article (1)

HeckRuler (1369601) | about 2 years ago | (#41324919)

So an intron is a.... NOP slide? [wikipedia.org]

The usual wave of people that distrust science (1)

HeckRuler (1369601) | about 2 years ago | (#41316547)

Any time there's a scientific discovery, or some news about what scientists have learned today, you get a wave of people that instantly baulk and assume that the entirety of scientific knowledge was just overturned and that everything that we've ever known was simply wrong. They see the new discovery as proof that the scientists were ignorant prior to the discovery.
Then you've got the crowd that assumes a discovery applies to 100% of whatever. For example, ENCODE has found function for some of the DNA that was considered junk. And sure enough the wave of ignorance came along and assumed that all DNA now had some purpose and the idea of junk DNA was wrong all along.

Informing the ignorant masses is hard. Informing the willfully ignorant masses is really hard.

Re:The usual wave of people that distrust science (1)

DMUTPeregrine (612791) | about 2 years ago | (#41319055)

Actually, they've found that some of the DNA that was considered junk is capable of functioning, but won't be activated during any normal operation of the cell. It's still junk.
Programming analogy:
while (false) {
      var=5;
}
The "var=5" is functional, if called it will set var to 5. It's also junk, since it will never be called.
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