Confusion and Criticism Over ENCODE's Claims

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."

Comments

I used to care about science journalism

[BMOC]

...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

[Anonymous Coward]

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

[oldhack]

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

The selfish gene.

[Hatta]

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.

Isn't it obvious?

[crow]

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:Sounds more like fighting over sacred cows

[tehdaemon]

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

No. Just no.

[shiftless]

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.