Confusion and Criticism Over ENCODE's Claims 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."
frosty piss (Score:2)
Patent Trolls seem analogous to /.
I used to care about science journalism (Score:5, Insightful)
...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 (Score:4, Interesting)
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.
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Yes... but please stop ruining my day further...
*cries*
The selfish gene. (Score:3)
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 (Score:2)
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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 (Score:5, Informative)
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
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Isn't it obvious? (Score:3)
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.
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No. Just no. (Score:2)
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.
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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?
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So do we really know that it's DNA that does aging?
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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 k
in other news (Score:2)
an article calling ENCODE's definition of functionality 'broad to the point of being fully patentable'
let the human gnome patent trolling begin.
Favorite quote from the article (Score:2)
"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?
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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
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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):
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The usual wave of people that distrust science (Score:2)
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 tha
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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.